Water column inshore/shallow and offshore/deep zone area proportions and layer thicknesses; seabed habitat area proportions and sediment properties:

The depth boundary between deep and shallow layers was determined using vertical diffusivity values from NEMO-MEDUSA (Yool, Popova, and Anderson 2013) and mixed layer depth from Globcolour (www.globcolour.info/). Shallow-deep layer division was set at 50m, with a bottom depth of 500m for the deep layer. The overhang extends up to a maximum depth of 500m, covering the spatial area between the 500m and 1000m isobaths (without seafloor). In the coastal zone, the polygon is defined for areas shallower than 50m or within 20 km of the coast. Seabed habitat proportions and sediment properties were derived from data by the REVIZEE Program (Figueiredo and Tessler 2004) and BNDO.

Parameters for relationship between median grain size, sediment porosity and permeability. Permeability is used as the basis for estimating hydraulic conductivity which is a parameter in the representation of sediment processes in the model:

Porosity (proportion by volume of interstitial water) and permeability of each sediment habitat were derived from median grain sizes using empirically-based relationships.

\[log_{10}(porosity) = p_3 + p_4\left(\frac{1}{1+e^{(\frac{-log_{10}(D_{50})-p_1}{p_2})}}\right)\] D₅₀ = median grain size (mm); parameters p₁ = -1.227, p₂ = -0.270, p₃ = -0.436, p₄ = 0.366 (Heath et al. 2021)

\[permeability = 10^{p_5}∙D_{50}^{*p_6}\]

where D₅₀* = 0.11 ≤ D₅₀ ≤ 0.50 p₅ = -9.213, p₆ = 4.615 (Heath, Wilson, and Speirs 2015).

These relationships are coded into the StrathE2E2 R-package with the parameters in the csv setup file for the SBS model. The parameters are probably a reasonable starting point for any future model of a new region. Derivation of the parameters is described in the following text sub-sections.

Parameters for in-built relationship between sediment mud content, and slowly degrading (refractory) organic nitrogen content of seabed sediments (see description in this document):

Values for each sediment type derived from parameterised relationships between total organic nitrogen content of sediments (TON%, percent by weight), mud content (mud%, percent by weight) and median grain size (D₅₀, mm).

\[mud\% = 10^{p_7}∙𝐷_{50}^{𝑝_8}\] p₇ = 0.657, p₈ = -0.800

\[TON\% = 10^{𝑝_9}∙mud\%^{𝑝_{10}}\]

p₉ = -1.965, p₁₀ = 0.590

Proportion of TON estimated to be refractory = 0.9

These relationships, along with their parameters, are documented in the North Sea implementation of the StrathE2E2 package (Heath et al. 2021). While there may be regional variations, these relationships serve as a reasonable starting point for the SBS implementation. The StrathE2E2 R-package encodes these relationships, with the parameters specified in the CSV setup file. Derivation of the parameters is described in the following sub-sections.

Assimilation efficiencies for each living guild in the model.

Fixed parameters defining the proportion of ingested mass of food that contributes to new body tissue, after subtracting defecation and the metabolic costs of digestion and synthesis (Heath 2012).

Biomass loss rates due to temperature-dependent metabolism for each living resource guild.

Proportion of biomass lost to ammonia per day due to non-feeding related metabolism at a given reference temperature. Rates for individual guilds broadly related to typical body mass of representative species. Temperature dependency following a Q₁₀ function.

Q₁₀ values for temperature dependent processes, and the Q₁₀ reference temperature.

Separate Q10 values for autotrophic uptake of nutrient, heterotrophic feeding, and heterotrophic metabolism based on literature data.

Light intensity required to saturate autotrophic nutrient uptake.

Light saturation intensity for nutrient uptake cannot be treated as a fitted value since it is confounded with other uptake parameters. Value estimated from survey of laboratory experiments.

Annual weight specific fecundities of planktivorous and demersal fish guilds and the two benthos guilds in the model (suspension/deposit feeders and carnivore/scavenge feeders).

Guild-level values derived by surveying the literature.

Harvestable biomass density threshold for each resource guild.

The living resource guilds in the model represent a mixture of harvestable and non-harvestable species, especially the invertebrate guilds. The density threshold parameter sets a limit for the guild biomass below which the harvestable species are assumed to be exhausted. Values set from analysis of trawl, plankton and benthos survey species biomass compositions.

Minimum inedible biomass of carnivorous zooplankton.

The carnivorous zooplankton guild is a key component of the food web, predated on by all the fish and top-predators. However it represents an extremely diverse range of fauna many of which are not edible in significant quantities by the guild predators, e.g. scyphomedusae. A minimum edible threshold is set to ensure that the guild as a whole cannot be extirpated by predation. The value is a rough estimate of scyphomedusae biomass.

Spawning and recruitment start and end dates for fish and benthos

We gathered the spawning and recruitment periods for each guild based on literature regarding the main species, described below. In the model the annual weight-specific fecundity is assumed to be shed uniformly between the start and end dates of spawning. The annual cohort of larvae/juveniles of each fish and benthos guild is assumed to recruit to the settled stage at a uniform daily rate between the start and end dates.

Planktivorous

For the planktivorous guild, we gathered data on the most caught species, Brazilian sardinella (Sardinella brasiliensis). The closed fishing season in SBS is set from November 1st to February 15th until 2019 (IBAMA (2009)), to cover the spawning period, and from June 15th to July 31th to protect the recruitment period. However, in 2020 the closed season changed to October 1st to February 28th to cover a large spawning period and better align with the species’ reproductive patterns (IN Nº 18, IBAMA, 2020). The spawning period occurring in austral spring and summer and the recruitment in winter also aligns with the literature (Cergole, Saccardo, and Rossi-Wongtschowski (2002); Moraes et al. (2012); Pio and Schwingel, 2012). We also check that the reproductive period of the second most caught planktivorous species, the Atlantic thread herring (Opisthonema oglinum), coincides with the reproductive cycle of S. brasiliensis, along with other small pelagic species (Feltrim and Schwingel, 2005; Petermann and Schwingel (2016)). Based on that, and to align with both closed seasons settled in SBS, we defined the spawning period of Planktivorous guild from October 1st to February 10th, and the recruitment from June 15th to August 15th.

Figure 4: Life cycle of the Brazilian sardine (Sardinella brasiliensis). Adapted from Gouveia (2016) and Soares et al. (2011).

Extra-domain stock biomass of migratory, and the proportion invading the domain each year. Start and end dates for the annual invasion, and start and end dates for the emigration. (see description below).

The main migratory fish species undertaking a seasonal transit in SBS is the skipjack tuna (Katsuwonus pelamis). Data on the Atlantic stock biomass of the skipjack and others relevant migratory fish, the proportion entering the SBS and the timing of the migration, were derived from literature and stock assessments (Jablonski and Matsuura (1985); Soares et al. (2019); Arregui, Goñi, and Chifflet (2020); ICCAT (2023); Pauly, Zeller, and Palomares (2023)).

Data Imputation

Due to various missing values, a data imputation process was carried out, resulting in approximately 70.5% of the data originating from original sources, 23.9% from landing values with estimated fleet information, and 5.6% from estimations for both landings and fleets. The detailed methodology is outlined below and noted in the “Obs” column of the SBS fisheries database compilation.

Missing Fleets

In cases where landing values by species were available but without fleet details, the following imputation criteria were applied: a. If fleet information was available for the same species and state but for a different year, the proportion of landings by fleet for that species was used for the closest possible period. b. If fleet information was available for the same state and year but not for the same species, the proportion of landings by fleet for the most closely related species from the nearest available state was used. c. If fleet information was not available for the same state, year, and species, the proportion of landings by fleet for the closest available state, year, and most similar species was used.

(#fig:landings_guild)Landings per year and guild compiled for the SBS StrathE2E model

(#fig:landings_fleet)Guilds per fleet for the SBS StrathE2E model averaged 2010-2019 period

Table 6: Aggregation of the fishing fleets for the SBS StrathE2E model

Fleets StrathE2E SBS	Artisanal (%)	Industrial (%)
Traps (benthos)	53.89	46.11
Pink-shrimp trawlers	15.49	84.51
Seabob-shrimp trawlers	88.32	11.68
Fish trawl	1.86	98.14
Trap nets	69.09	30.91
Purse and beach seines	8.99	91.01
Bottom gillnet	41.48	58.52
Surface gillnet	86.82	13.18
Bottom longline	40.20	59.80
Surface longline and lines	27.79	72.21
Others/multiple gear	88.12	11.88
Pole and line	0.01	99.99

Cetaceans

For the cetacean guild, we utilized studies by Bertozzi and Zerbini (2002), Ott et al. (2002), Secchi, Kinas, and Muelbert (2004), Perez and Wahrlich (2005), Flach (2015), C. O. Fogliarini (2017), and Prado et al. (2021) for bottom gillnets with bycatch data on the franciscana (Pontoporia blainvillei), Guiana dolphin (Sotalia guianensis), common dolphin (Delphinus sp.), and other dolphins of the genus Stenella. Among the compiled studies, the highest bycatches were associated with bottom gillnet fishing targeting the monkfish (Lophius gastrophysus), occurring extensively in the offshore SBS Perez and Wahrlich (2005). Fishing targeting croaker, drum, and other demersal fish ranked second in estimated bycatch values Secchi, Kinas, and Muelbert (2004). Cetacean bycatch was particularly concerning in gillnet fisheries, with the critically endangered franciscana dolphin highlighted, as reported by OCEANA (2024).

For surface gillnets, we referred to studies by Ott et al. (2002), Secchi, Kinas, and Muelbert (2004), Mäder, Sander, and Balbão (2006), Sidou (2008), Fruet et al. (2010), Marigo and Giffoni (2010), Domiciano (2016), and C. O. Fogliarini (2017). In addition to the dolphin species caught in bottom gillnets, surface gillnets also resulted in bycatch of bottlenose dolphins (Tursiops truncatus), Atlantic spotted, spinner, and striped dolphins (Stenella frontalis, S. longirostris, and S. coeruleoalba), pygmy killer whale (Feresa attenuata), melon-headed whale (Peponocephala electra), and long-finned pilot whales (Globicephala melas). Surface gillnets targeting sharks, tuna, and mullets across the SBS contributed significantly to the annual bycatch.

The total cetaceans bycatch from both the gillnets fleets was estimated at 25.19 tons per year - 14.51 from surface and 10.68 from bottom gillnet.

Seabirds

For the seabird guild, we compiled sources of Perez and Wahrlich (2005), Luis Gustavo Cardoso et al. (2011), and C. O. Fogliarini (2017) for bottom gillnets, recording bycatch of the species: Magellanic penguin (Spheniscus magellanicus), and petrels (Daption capense, Procellaria aequinoctialis, Puffinus griseus, and P. gravis). The fleet targeting monkfish was responsible for the major petrel bycatch, followed by fleets targeting croaker and other demersal fish, with incidental captures of penguins.

For surface gillnets, we used the sources of Luis Gustavo Cardoso et al. (2011), J. O. Branco et al. (2014), and C. O. Fogliarini (2017). The anchovy fishery in Rio Grande do Sul yielded the highest seabird bycatch. The incidental capture of Magellanic penguins in both surface and bottom gillnets is significant and considered the primary source of adult mortality in their wintering areas Carine Oliveira Fogliarini et al. (2019). In addition to the previously mentioned seabirds in gillnets, surface longlines and lines also recorded bycatch of other petrels (Macronectes giganteus, Oceanites oceanicus, Puffinus puffinus, and Calonectris borealis), and albatrosses (Diomedea dabbenena and D. exulans). For surface longline and line data, we used sources such as Olmos, Neves, and Bastos (2001), Bugoni et al. (2008), J. O. Branco et al. (2014), and Gianuca et al. (2020). Different fisheries targeting large pelagics fish were responsible for bycatch across the SBS offshore and overhang zones. Gianuca et al. (2020) observed that albatross and petrel bycatch in SBS fleets often involved birds that were accidentally caught, mutilated, or killed and discarded. Bycatch in various longline fleets is widespread but largely undocumented, posing a significant threat to seabirds. For bottom longlines, we referred to Neves et al. (2006), which reported low bycatch values for petrels.

This compilation resulted in a total seabird bycatch of 5.51 tons per year - 3.7 from surface longline and lines, 1.44 from bottom gillnet and 0.37 from surface gillnet.

Pinnipeds

Pinnipeds in the SBS occurs in the South region, in Rio Grande do Sul. We used Machado (2015), which documented bycatch of the South American sea lion (Otaria flavescens) by the pair trawl fleet in this region. Mäder, Sander, and Balbão (2006) provided estimates of bycatch for O. flavescens and fur seals (Arctocephalus australis and A. tropicalis) in surface gillnets. Unlike cetaceans and seabirds, the highest mortality of pinnipeds due to fishing does not occur onboard but through subsequent interactions with ghost nets Mäder, Sander, and Balbão (2006). We considered then an annual bycatch of 1.53 tons - 1.07 from surface gillnet and 0.46 from fish trawl.

Fishing effort

Fishing effort data for each fleet are required as inputs to the model in terms of seconds of activity per mˆ2ˆ per day. Although the SBS contains apparent annual fishing effort data from the National Fishing Vessel Tracking Program (PREPS) via the Global Fishing Watch (GFW) map interface, these data only records large industrial vessels and do not align with the fleets defined for the StrathE2E SBS model. Therefore, we used fishing days data from state-specific monitoring programs, later converting them to fishing hours. The steps taken to reach the final unit are described below.

Fleet Distribution per habitat

Fleet distribution in each habitat was allocated by combining information from PMAP reports with the sediment habitats. Maps and associated text, often specifying the locations and isobaths with the most fishing activity, was used to allocate the fleets in each habitat, assisted by georeferenced sediment habitats.

Top-predators

Cetaceans

For the Cetaceans guild we utilised the density and abundance estimates from the Cetacean Monitoring Project in the Santos Basin (Projeto de Monitoramento de Cetáceos na Bacia de Santos - PMC-BS) (Petrobras, 2021) based on both onboard and aerial monitoring conducted over five years of effort. General data were available for mysticetes and delphinids, as well as specific data for three species with sufficient sample sizes: the humpback whale (Megaptera novaeangliae), Atlantic spotted dolphin (Stenella frontalis), and bottlenose dolphin (Tursiops truncatus).

The study area of the PMC-BS encompasses a significant portion of the SBS, extending from Cabo Frio-RJ to Florianópolis-SC and down to 2000 m depth. Although the covered isobath surpasses the domain of the present model, it is noted that most species are found in the shelf region rather than the oceanic region. The humpback whale is a species that can be found at greater depths; however, the average sighting depth was approximately 420 m, indicating that the estimated density can be attributed to the SBS region considered in this StrathE2E baseline model. We used data from campaigns 1 to 9, representing data collected between 2015 (PMC-BS start year) and 2019 (the end year of the StrathE2E SBS baseline period), and averaged the number of individuals per km² for this period and for both aerial and overboard monitoring methods. We then compiled the average weight of the main cetacean species in the region using the average weight of females and males as reported in Christensen (2004). The number of individuals was multiplied by the average weight to obtain the biomass per km². Subsequently, we multiplied this by our study area (311,733 km²), which is slightly larger than that of PMC-BS, as it includes the state of Rio Grande do Sul. We assumed cetacean abundance to be consistent throughout the southern SBS, given that the same species persist across the entire area.

To estimate the weight of “Other Mysticeti,” we utilized the average weight of Bryde’s whale (Balaenoptera brydei) due to its significant presence in the region as reported in the PMC report. This species is also the only large whale observed in Brazilian waters year-round. Additionally, other whale species recorded in the report as present in the SBS include Eubalaena australis, Balaenoptera acutorostrata, B. bonaerensis, B. borealis, and B. physalus. For the weight of “Other Delphinidae,” we used the average weight of the primary delphinid species in the region: Delphinus delphis, Feresa attenuata, Globicephala macrorhynchus, Grampus griseus, Sotalia guianensis, Stenella attenuata, S. clymene, S. longirostris, and Steno bredanensis. We also used the specific weights of M. novaeangliae, S. frontalis, and T. truncatus and their respective abundances for the biomass calculation.

We estimated an annual biomass of 0.12 t/km², totaling 36,788.93 tons. We also utilised the PB ratio (0.050) from Gasalla and Rossi-Wongtschowski (2004), encompassing the species Sotalia fluviensis, Steno bredanensis, Pontoporia fluviatilis, Balaenoptera edeni, Stenella frontalis, and Tursiops truncatus.

Figure 10: Two cetaceans species inclued in the Cetaceans guild in the SBS model: Humpback whale (above) and Atlantic spotted dolphin (below). Illustrations by NOAA Fisheries and Dawn Witherington.

Pinnipeds

Regarding pinnipeds, the sea lions Otaria flavescens, Arctocephalus australis, and Arctocephalus tropicalis are the most abundant species in Brazil, predominantly inhabiting the Rio Grande do Sul region (Santos et al., 2012; Silva, 2004). The only nearby ecosystem models with biomass estimates found were those by Bergamino et al. (2012), who estimated O. flavescens biomass at 0.018 t.kmˆ2ˆ in the Rio de la Plata estuary and adjacent oceanic areas, and Reinaldo et al. (2016), who evaluated O. flavescens and A. australis at 0.021 t.kmˆ2ˆ on the Patagonian shelf. Despite the lack of studies evaluating pinnipeds biomass in SBS, it is expected that a portion of these populations enters the model for feeding and resting. Silva (2004) provides population estimates of O. flavescens and A. australis in the two Brazilian pinniped refuges, at 455 and 277 individuals, respectively. The average weights of each species were used to estimate our model biomass. Due to the lack of information regarding the population size of A. tropicalis in Brazil, its population was considered equivalent to that of A. australis and added to the total biomass of the guild. The PB ratio used was 1.04, as reported by Reinaldo et al. (2016).

Demersal fish

The biomass of the demersal guild in the SBS was estimated using a range of sources for the main species in the region, which included 39 taxa with one or more species. Among the sources used are the outputs parameters of Ecopath models by Gasalla and Rossi-Wongtschowski (2004), Gasalla et al. (2007), and Bornatowski et al. (2018), adjusting the area when necessary if the species is predominant in a specific zone of the model; Haimovici et al. (2009) bottom trawl surveys from the REVIZEE cruise, and Sea Around Us stock assessments (averaged from 2010-2018 or the last year available). For the SAU stock assessments, we ensured that the marine ecoregion matched the SBS, and in cases where it covered a broader region (e.g., the entire Brazil EEZ), we adjusted the biomass using the catch ratios of the broader region compared to our catches. Local stock assessments are rare but we include those by Pio (2015) and Sant’Ana and Perez (2016). As a result, we estimated an annual demersal fish biomass of 3.30 t.km-², or a total of 1,029,853 tons, in the SBS. More details about the considerations for the main species are provided below.

The major commercial demersal fishes (constituting over 80% of our landings) comprise the species Micropogonias furnieri, Umbrina canosai, Urophycis spp., Cynoscion guatucupa and C. jamaicensis, Prionotus punctatus, Trichiurus lepturus, Paralichthys spp., Merluccius hubbsi, Macrodon atricauda, and M. ancylodon.

For the Whitemouth croaker (M. furnieri), the most caught demersal species, we derived the biomass estimated from Pio (2015), summing the Southeast and South stocks for the average 2010-2012, which resulted in approximately 118,000 tons. Due to the lack of available P/B values in the literature, the most recent total mortality (Z) of 0.6 from Haimovici et al. (2021) was used.

The Argentine croaker U. canosai, another commonly caught species, was assessed by SAU using Haimovici and Cardoso (2017) as the source for relative biomass. The most recent Z estimate of 0.86 from Haimovici et al. (2022) was used. Other exploited sciaenid species include the weakfishes C. guatucupa, C. jamaicensis, M. atricauda, and M. ancylodon, which have economic and ecological contributions in the SBS. Rough estimates for each species were made considering the ratio between reported biomass and catches in the SAU and our catch. PB values from other ecosystem models (Gasalla and Rossi-Wongtschowski, 2004) for the sciaenids group were used.

The mullet (Mugil liza) is considered heavily overfished according to both SAU and OCEANA assessments. We used the biomass from the stock assessment for 2015 by Sant’Ana & Kinas (2016), which remained almost constant until 2019 (UNIVALI, 2020), and points that the mullet stock is overfished and experiencing overfishing. The PB used was from Gabin et al. (2014) total mortality Z.

The hake (Merluccius hubbsi), cutlassfish (Trichiurus lepturus), and Brazilian codling (Urophycis spp.) are highly abundant species in the offshore and overhang zones of the model (Haimovici et al., 2008). These species hold commercial importance and are considered overfished (B<Bmsy), as indicated by Cardoso et al. (2022). Their biomass estimates and for the remaining major commercial species were sourced from ecosystem models by Gasalla et al. (2007), Bornatowski et al. (2018), and bottom trawl data from the REVIZEE cruises (Haimovici et al., 2008). The “Other demersal fishes” group in the Gasalla et al. (2007) model encompasses approximately 20 species recorded in bottom trawl surveys (Haimovici et al., 2006), all of which show high biomass levels.

For non-commercial species, deep-ocean bentho-pelagic fish characterised as demersal were included, also exhibiting substantial biomass (e.g., Caelorinchus marinii, Xenolepidichthys dalgleishi from Bornatowski et al. (2018)). PB values for these species were derived from the same source. Boarfish (Antigonia capros) and rosefish (Helicolenus spp.) biomass, along with their PB values, were taken from the Gasalla et al. (2007) model. Additionally, the silvery John dory (Zenopsis conchifer) was considered based on REVIZEE bottom trawl surveys conducted off southern Brazil (Haimovici et al., 2009), with PB values sourced from Nascimento et al. (2010).

The PB value of 0.76 was used as well as target data, based on the average PB of the key species/groups that account for 95% of the biomass, with the SD value of 0.47.

Planktivorous fish

Recent assessments of planktivorous fish biomass are limited in the literature. For the purpose of model parameterization, the biomass of the planktivorous guild in the SBS was estimated using a variety of sources, including other models and hydroacoustic surveys for key SBS species. We considered an annual biomass of 9.72 t/km², totaling 3,029,116.75 tons, which included 16 taxa representing one or more species. Further details regarding the main species are provided below.

In the compiled fisheries data, the Brazilian sardine (Sardinella brasiliensis) was the most caught species, even when considering all catches from the SBS StrathE2E guilds. Despite several advances in the knowledge of this species over recent years, there are no recent official biomass estimates, and is considered “Data Deficient” by the International Union for the Conservation of Nature (IUCN) (Di Dario, 2018). We applied a biomass value of 3.55 t/km², as reported by Soares (2021), which was derived from unpublished data by the Scientific Committee (2021), to our study area. The Atlantic thread herring (Opisthonema oglinum) ranks as the second most frequently caught species, and we derived a rough estimate based on the ratio between reported biomass and catches in the SAU for Brazil’s EEZ, adjusting for our SBS catches. The PB ratio for both species was obtained from Bornatowski et al. (2017) under the “Engraulidae and Clupeidae” group. The planktivorous biomass also includes other forage fish species such as Bregmaceros atlanticus, Bregmaceros cantori, Scomber spp., jacks (Caranx spp.), and other Engraulidae and Clupeidae species. Biomass estimates for these taxa were derived from Pauly, Zeller, and Palomares (2023), Gasalla et al. (2007), Haimovici et al. (2008), or in the last case, estimated based on the proportion of biomass to catch of ecologically similar species. PB values were sourced from Gasalla and Rossi-Wongtschowski (2004), Gasalla et al. (2007), and Bornatowski et al. (2018).

Among non-commercial species, the argentine anchovy (Engraulis anchoita) represents a significant stock shared with Uruguay and Argentina (Vaz-dos-Santos et al., 2007). In the SBS, its commercial exploitation is minimal, and the species exhibits a high capacity to replenish its biomass, a typical characteristic of small pelagics (Cooke and Madureira, 2012). For this species, we used biomass data from Cooke and Madureira (2012) and the PB ratio from Bornatowski et al. (2017). The mesopelagic pearlside (Maurolicus stehmanni) also contributes substantially to SBS fish biomass, being particularly abundant on the outer shelf and continental slope (Madureira and Rossi-Wongtschowski, 2005; Rodrigues-Ribeiro et al., 2021). As a forage species with a short life span, rapid growth, and a dietary preference for zooplankton, M. stehmanni was classified here within the planktivorous guild (Ribeiro, 1996; Almeida, 2001). Although not directly targeted by fisheries, it plays a crucial trophic role, serving as prey for tuna, squid, and demersal fish (Bornatowski et al. (2018)). We applied biomass values from Gasalla et al. (2007) from their Ecopath model for the SBS region between 100 and 1000m, which were based on hydroacoustic surveys conducted by Madureira et al. (2005). Additionally, we included biomass estimates and PB values for other planktivorous mesopelagic species, including 18 species from the Gasalla et al. (2007) model, with 61% of the biomass in this group comprising other Myctophidae species.

The PB value of 1.36 and SD 0.28 was used as well as target data, based on the average PB of the key species/groups that account for 95% of the biomass: S. brasiliensis, E. anchoita, M. stehmanni, along with the groups classified as other forage species and other mesopelagic planktivores.

Carnivorous and scavengers benthos

We aggregated biomass data for commercial and non-commercial species within the CS Benthos guild, noting that non-commercial species exhibited the highest densities. Among the commercial species, the shrimps Xiphopenaeus kroyeri, Farfantepenaeus spp., Artemesia longinaris, Pleoticus muelleri, and Litopenaeus schmitti are the most important, comprising 71.7% of the guild’s landings. The biomass of the pink shrimp Farfantepenaeus paulensis Farfantepenaeus subtilis. was available for the SBS from the Pauly, Zeller, and Palomares (2023) assessments for 2010-2018. For the other shrimp species, we made a rough estimate by considering the ratio between reported biomass and catches in the Pauly, Zeller, and Palomares (2023) for the Brazilian EEZ, compared to our SBS catches for the 2010-2018 average. The PB values for both species were derived from Gasalla and Rossi-Wongtschowski (2004).

Crabs are also significantly caught in the SBS. As we did not found studies evaluating the biomass of individual crab species in the region, we used the biomass values from the model by Nascimento et al. (2010), which derives from the REVIZEE cruises prospection (Amaral and Rossi-Wongtschowski, 2004) and includes various species of commercial and non-commercial crabs (e.g., Chaceon spp., Portunus spp., Euprognatha sp., Scyllarides deceptor, among others).

Two main species of lobsters occur in the region, Metanephrops rubellus and Panulirus argus. The biomass of P. argus was roughly assumed to be the same as that from Eastern Brazil in the SAU stock assessment for the 2010-2018 average. No biomass assessments for M. rubellus were found up to the date of this study. For model parameterization purposes, we made a rough estimation using the biomass and catch of Panulirus argus applied to our SBS M. rubellus catches.

Octopuses from the family Octopodidae are significantly captured in the SBS, with Octopus vulgaris being the most abundant species along the SBS coast (0–100 m depth) (Haimovici et al., 2009). In the absence of specific biomass estimates for octopuses, we used the biomass and PB values from the “Predator molluscs” group in the Nascimento et al. (2010) ecosystem model, which includes octopuses along with many other noncommercial CS benthic species. The same source was used for the biomass and PB values of predator crustaceans (Hemisquilla brasiliensis, Squilla sp.), deep-sea shrimp (Alpheus spp., Heterocarpus spp., Rhynchocinetes spp., Acanthephyra spp., Aristaeopsis edwardsiana, among others), and benthic omnivorous invertebrates (Isopoda, Amphipoda, Chaetognatha).

This resulted in a biomass for the CS benthos guild of 8.08 t.km-², totaling 2,517,712.48 tons. The PB value of 3.51 and SD 2.44 was used as well as target data, based on the average PB of the key species/groups that account for >95% of the biomass.

Suspension and deposit benthos

The most important commercial species in the SD guild are the oyster Crassostrea rhizophorae and the mussel Perna perna, accounting for 69.7% of our landings. For both species, we used the biomass from the SAU stock assessment for the SBS region from the 2010-2018 average. Non-commercial SD benthos comprise most of the guild’s biomass. We used the biomass of Polychaeta, Infauna, Detritivorous invertebrates, and Bivalves from the Nascimento et al. (2010) ecosystem model, derived from the Amaral and Rossi-Wongtschowski (2004) REVIZEE cruises, and the PB values for each group from the same source.

This resulted in a biomass for the SD benthos guild of 31.68 t.km-², or 9,875,197.3 tonnes. The PB value of 5.8 was used as well as target data, based on the average PB of the key species/groups that account for 95% of the biomass, and the SD value of 6.09.

Carnivorous and scavengers zooplankton

For the carnivorous zooplankton guild, we considered squids and gelatinous zooplankton as primary representatives. Haimovici et al. (2008) provided a survey of the biomass of the squid Loligo plei on the outer shelf, covering depths of 100-600 m. However, caution was advised as the surveys did not include the inner shelf, where most of this species’ biomass is found (Perez, 2002). To include squids on the inner shelf, we utilized Loligo spp. biomass data of 5.28 t/km² from Gasalla and Rossi-Wongtschowski (2004), scaled by the study area. PB values were sourced from Vera (2010). We also considered the biomass and PB values of the Argentine shortfin squid (Illex argentinus) from Gasalla et al. (2007), an abundant species found at greater depths.

Regarding planktonic cnidarians, over 300 species are documented in the SBS (Miodeli, 2011), with species like the scyphomedusae Lychnorhiza lucerna exhibiting substantial biomass in shallow coastal areas (Nogueira Júnior and Haddad, 2017). However, gelatinous zooplankton remains one of the least studied groups in Brazil (Lopes, 2007). The latest quantitative assessment of gelatinous zooplankton biomass was conducted by Nogueira-Junior et al. (2010), focusing on the Macromedusae biomass of Hydrozoa, Cubozoa, and Scyphozoa. We extrapolated total biomass data, originally sampled in Florianopolis and converted into tonnes, to cover the entire SBS area by dividing it by the netting route area (km²). Given the lack of local data, we applied the PB ratio for jellyfish from the World’s Large Marine Ecosystems Ecopath model (Christensen et al., 2014).

The PB value of 5.15 was used as well as target data, based on the average PB of the aforementioned species, with SD value of 4.27.

Omnivorous zooplankton

No public databases of zooplankton biomass were identified for significant resolution of the SBS region, which is largely unstudied, particularly for certain taxa (Nogueira and Brandini, 2018). Recent studies have been conducted over short durations, primarily concentrating on estuarine and coastal areas, such as Santos (Miyashita et al., 2009), Ubatuba (Melo-Junior et al., 2016), and Cabo Frio (Dias et al., 2015). Nogueira and Brandini (2018) highlighted the presence of nearly 800 zooplanktonic invertebrate species within the SBS and the higher zooplankton biomass in coastal areas. Herbivorous copepods comprise the majority of the zooplankton community on the shelf and represent a direct link to fishery food webs (Brandini et al., 1997; Lopes et al., 2006).

Melo-Junior et al. (2016), when studying the copepod community off Ubatuba, pointed out that the dominant copepods were immature copepodids and small adults of species belonging to the genera Oncaea, Temora, Paracalanus, Clausocalanus, Oithona, and Onychocorycaeus, a pattern that can be representative of the entire SBS The integrated average biomass for the water column was 18.39 mg.mˆ-3ˆ, which converted by wet weight and using the local depth of 40 m results in 3,679 g/m². In the Miyashita et al. (2009) study for the Santos estuarine inner shelf, the average copepod biomass was 4.17 g.mˆ-2ˆ (converted by wet weight and using the local depth of 50 m), and was higher in the summer.

In the absence of a comprehensive study covering the entire SBS, we opted to use biomass and PB data from modeling conducted by Gasalla and Rossi-Wongtschowski (2004) and Gasalla et al. (2007). Given the consistent SBS zooplankton inshore-offshore gradient, and considering that Gasalla and Rossi-Wongtschowski (2004) study area extends to coastal waters up to 100 m, we multiplied their reported biomass of 10.5 t.kmˆ-2ˆ by the area of their study model (97000 kmˆ2ˆ). Additionally, we applied the biomass figure of 3.8 t.kmˆ-2ˆ from Gasalla et al. (2007), covering depths from 100 to 1000 m, to the remaining area of our model (214733 kmˆ2ˆ). Gasalla and Rossi-Wongtschowski (2004) specify that the zooplankton biomass includes copepods, cladocera, chaetognatha, appendicularia, sergestids, luciferids, and salps. Thus, combining the findings from both studies, we arrived at a final estimate of 5.88 t.km-² for our domain, allocated to the Omnivorous Zooplankton guild.

Seabirds

Across the studies reviewed, demersal fish is reported as the dominant component of seabird diets in the SBS, generally accounting for over 50% of the prey consumed, followed by small pelagic fishes, cephalopods and/or bivalves. For instance, Branco et al. (2005) found that demersal fish, primarily Sciaenidae, comprised 50% of the diet of Sula leucogaster, followed by benthic species such as shrimp with 26.5%, and small pelagic fish like sardines (Clupeidae and Engraulidae) accounting for 23.5%. Similarly, Mancini et al. (2023) reported that demersal species comprised 54.4% of S. leucogaster’s diet, while small pelagic fish contributed 42.6%. The diet of Larus dominicanus in Paraná, as studied by Miotto et al. (2017), was also dominated by demersal species, with Paralonchurus brasiliensis and Stellifer rastrifer together accounting for more than 79% of the diet. In Silva-Costa and Bugoni (2013), small demersal fish were the primary prey for Larus dominicanus, followed by bivalves. Bugoni and Vooren (2004) highlighted the importance of demersal fish for Sterna hirundo during the winter in Rio Grande do Sul, constituting 93% by mass. Likewise, Oliveira et al. (2019) found that the diet of Nannopterum brasilianus in Rio Grande do Sul primarily consisted of demersal fish, with occasional consumption of the squid Doryteuthis plei. Colabuono and Vooren (2006) also found that demersal fish were significant for albatross species (Thalassarche spp.), comprising 47.2% to 100% of their diet, though the diet of petrels (Procellaria spp.) was predominantly cephalopods (77.3–95.9%).

Numerous studies across the SBS indicate that the prevalence of demersal fish in the diet of seabirds is closely related to fishery discards, particularly from trawl fisheries (Bugoni and Vooren, 2004; Colabuono and Vooren, 2006; Traversi and Vooren, 2010; Carniel and Krul, 2012; Silva-Costa and Bugoni, 2013; Miotto et al., 2017). Carniel and Krul (2012) observed that 90.3% of seabird interactions with fishing operations involved feeding on trawling discards. Colabuono and Vooren (2006) reported that 40% of the fish consumed by seabirds were derived from fishery discards, most of which were juvenile demersal individuals below the marketable size and a large proportion of trawling bycatch. Similarly, Branco (2001) found that in Santa Catarina, discards from seabob shrimp fisheries—mostly small demersal fish—accounted for 84% of the diet of seabirds. Similarly, Traversi and Vooren (2009) found that 80% of the total prey mass consumed by Sterna hirundo came from demersal fish discards.

Based on the dietary proportions reported in these studies, we assumed that fishery discards account for 50% of the seabird diet, with 30% composed of other demersal fish, 10% of planktivorous fish, 2% migratory fish, and the remaining 8% distributed among squids, CS benthos, and other prey groups ((Table 10). These proportions were integrated into the target data for our model to better simulate seabird feeding behaviours and interactions with the SBS ecosystem.

Cetaceans

We focused on dolphins diets, as Mysticeti (i.g. humpback whales), do not typically feed during their breeding season or migrations through the SBS. Santos et al. (2002) found that squids was the main prey in the common dolphin (Delphinus capensis) and bottlenose dolphin (Tursiops truncatus), followed by demersal sciaenid fish, particularly Stellifer rastrifer, and shrimps. Similarly, Bassoi et al. (2020) observed that franciscana dolphins (Pontoporia blainvillei) in southern Brazil primarily consumed the squid Loligo sanpaulensis and demersal fish species such as Cynoscion guatucupa. The diet of Guiana dolphins (Sotalia guianensis) is also composed of sciaenid fishes such as Paralonchurus brasiliensis, and the squid Doryteuthis plei (Lopes et al., 2012). Aggregating diet data from Lopes et al. (2012) into the StrathE2E guilds, we find that cephalopods (Doryteuthis plei and Loliguncula brevis) contributed 36.7% to the diet, while demersal fish (e.g., Sciaenidae, Trichiuridae, Mugilidae) 30.55%, and planktivorous fish (Clupeidae, Engraulidae) represented 32.7%.

In the case of franciscana dolphins (Pontoporia blainvillei), Campos et al. (2020) reported that their diet is dominated by the planktivorous fish Pellona haroweri, besides squid (Doryteuthis plei) and demersal fish (Isopisthus parvipinnis), showing a preference for both pelagic and demersal prey. Henning et al. (2018) further supported these findings, noting that the most important species in the diet of franciscana dolphins were P. harroweri, D. plei, P. brasiliensis, and I. parvipinnis, with planktivorous prey comprising 34.92%, cephalopods 37.3%, and demersal fish 39.14%. Melo et al. (2009) examined the feeding habits of six delphinid species, were cephalopods—particularly the squid Loligo plei—comprised 71.4% of the total prey, while teleosts 28.6%.

The feeding preference for cephalopods and demersal fish, with a smaller proportion of pelagic fish and CS benthos for some species, was consistently noted across the cetacean species in the reviewed studies. Based on the reported data, we assumed that demersal fish comprises 35% of the cetaceans’ diet, planktivorous fish 15%, migratory fish 5%, with the remaining portion distributed among squids, CS benthos, and other prey groups ((Table 10). These proportions were incorporated into the model to better simulate cetacean feeding behaviours within the SBS ecosystem.

Pinnipeds

Based on stable isotope analysis, Zenteno et al. (2015) found that South American sea lions (Otaria flavescens) primarily consumed demersal fish, with juveniles incorporating a higher proportion of pelagic prey compared to adults. Machado et al. (2018) also observed that demersal Sciaenid fish dominated the O. flavescens diet (93.37%), with key species including Paralonchurus brasiliensis, Micropogonias furnieri, and Macrodon atricauda. In smaller amounts, migratory fish such Pomatomus saltatrix (2.02%) and cephalopods (0.05%) were also recorded.

In contrast, South American fur seals (Arctocephalus australis) were found to predominantly consume coastal small pelagic species, such as Anchoa marinii (~55%), demersal fish (mainly sciaenids, ~25%), along with cephalopods (mainly Doryteuthis sanpaulensis, ~20%), according to Lima et al. (2023). For sub-Antarctic fur seals (Arctocephalus tropicalis), offshore squids such as Ommastrephes bartramii and Illex argentinus (70.6%) formed the majority of their diet, complemented by pelagic fish such as Odontesthes bonariensis (11.8%) and smaller proportions of other prey items.

As O. flavescens is the most abundant pinniped in the SBS (see Section X), we primarily based the diet proportions in our model on their feeding habits but also accounted for the importance of small pelagic species and squids in the diet of A. australis and A. tropicalis. We assumed that 50% of the pinniped diet consists of demersal fish, 20% of pelagic fish, 2% migratory species, and the remaining proportion is distributed among squids and other prey types ((Table 10).

Table 10: Proportions of the fish guilds and discards in the diet of seabirds, cetaceans and pinnipeds considered as target data in the SBS model.

Migratory fish

According to the most recent assessments, Katsuwonus pelamis is neither overfished nor subject to overfishing (ICCAT, 2019a), a finding consistent with other tunas such as albacore (Thunnus alalunga) and yellowfin (Thunnus albacares) (ICCAT, 2016; 2019b).

To calculate the harvesting ratio, we divided the estimated catch (discussed in Section X) by the estimated biomass of the guild (outlined in Section Y). Note that some species (shark species, Ruvettus pretiosus, Lepidocybium flavobrunneum, Gempylus sp.) are part of the harvesting ratio of the guild although it is not harvested. Based on rough estimates derived from catch and biomass data used for model parameterization, we estimated a harvesting ratio for the SBS of 1.39E-04.

Demersal guild

Cardoso et al. (2022) reports a continuous decline over the last years in the ratio of annual biomasses to the Bmsy for most of the demersal stocks along the SBS. Despite the steady decline, most demersal stocks could have not collapsed yet likely due to life-history traits that favor resilience, such as early maturation and rapid growth (Chao et al., 2015). For the whitemouth croaker (M. furnieri), the most caught demersal species, Pio (2015) indicates relatively sustainable biomass levels in the SBS but unsustainability of the stock in the long term. The OCEANA Fishery Audit 2022 (Perez et al., 2022) and Haimovici et al. (2021) highlights a state of heavy overfishing in recent years, particularly for the South Brazil whitemouth croaker stock. The mullet (Mugil liza) is in a similar situation and is considered heavily overfished according to both SAU and OCEANA stock assessments.

To calculate the harvesting ratio, we divided the estimated catch (discussed in Section X) by the estimated biomass of the guild (outlined in Section Y). Note that some species (bentho-pelagic and deep-sea species) are part of the harvesting ratio of the guild although it is not harvested. Based on rough estimates derived from catch and biomass data used for model parameterization, we estimated a harvesting ratio for the SBS of 2.36E-04.

Planktivorous fish

A stock review conducted by OCEANA (2024) reports that the status of small pelagic fish stocks in the SBS remains unknown due to a lack of data.

To calculate the harvesting ratio, we divided the estimated catch (discussed in Section X) by the estimated biomass of the guild (outlined in Section Y). Note that some species (Engraulis anchoita and mesopelagic planktivorous such as Maurolicus stehmanni) are part of the harvesting ratio of the guild although it is not harvested. Based on rough estimates derived from catch and biomass data used for model parameterization, we estimated a harvesting ratio for the SBS of 9.06E-05.

Carnivorous and Scavenger Benthos

According to Cardoso et al. (2021), the stocks of Farfantepenaeus spp. and Pleoticus muelleri are currently overfished in the SBS, but no shrimp species evaluated are currently experiencing overfishing. Data regarding other SBS CS benthos stocks are rare in the literature. To calculate the harvesting ratio, we divided the estimated catch (discussed in Section X) by the estimated biomass of the guild (outlined in Section Y). Based on rough estimates derived from catch and biomass data used for model parameterization, we estimated a harvesting ratio for the SBS of 1.77E-05.

Suspension and deposit feeders benthos

Data regarding the SBS SD benthos stocks are rare in the literature. To calculate the harvesting ratio, we divided the estimated catch (discussed in Section X) by the estimated biomass of the guild (outlined in Section Y). Based on rough estimates derived from catch and biomass data used for model parameterization, we estimated a harvesting ratio for the SBS of 1.94E-07.

Carnivorous zooplankton

Data regarding the SBS CS zooplankton stocks are rare in the literature. To calculate the harvesting ratio, we divided the estimated catch (discussed in Section X) by the estimated biomass of the guild (outlined in Section Y). Based on rough estimates derived from catch and biomass data used for model parameterization, we estimated a harvesting ratio for the SBS of 2.73E-06.

Seabirds, cetaceans and pinnipeds

For the top-predators, we performed a rough estimate of the harvesting ratio by dividing the daily bycatch data (as applied in Section X) by the annual biomass estimate (referenced in Section Y). This calculation resulted in a harvesting ratio of 1.64E-05 for seabirds, 2.64E-05 for pinnipeds and 1.90E-06 for cetaceans.